Agent-Based Model of Genotype Editing

Chien-Feng Huang1, Jasleen Kaur2, Ana G. Maguitman3, Luis M. Rocha2*

1Los Alamos National Laboratory, P.O.Box 1663, Los Alamos, NM 87545
2School of Informatics, Indiana University, 1900 East Tenth Street, Bloomington IN 47408
3Universidad Nacional del Sur, Bahia Blanca, Argentina
*To whom correspondence should be addressed:

Citation: C. Huang, J. Kaur, A. Maguitman, L.M. Rocha [2007]."Agent-Based Model of Genotype Editing". Evolutionary Computation, 15(3): 253-89.

Access to reprint at Evolutionary Computation Journal site. The pre-print is available in Adobe Acrobat (.pdf) format only. Due to mathematical notation and graphics, only the abstract is presented here.


Evolutionary algorithms rarely deal with ontogenetic, non-inherited alteration of genetic information because they are based on a direct genotype-phenotype mapping. In contrast, in Nature several processes have been discovered which alter genetic information encoded in DNA before it is translated into amino-acid chains. Ontogenetically altered genetic information is not inherited but extensively used in regulation and development of phenotypes, giving organisms the ability to, in a sense, re-program their genotypes according to environmental cues. An example of post-transcriptional alteration of gene-encoding sequences is the process of RNA Editing. Here we introduce a novel Agent-based model of genotype editing and a computational study of its evolutionary performance in static and dynamic environments. This model builds on our previous Genetic Algorithm with Editing, but presents a fundamentally novel architecture in which coding and non-coding genetic components are allowed to co-evolve. Our goals are: (1) to study the role of RNA Editing regulation in the evolutionary process, (2) to understand how genotype editing leads to a different, and novel evolutionary search algorithm, and (3) the conditions under which genotype editing improves the optimization performance of traditional evolutionary algorithms. We show that genotype editing allows evolving agents to perform better in several classes of fitness functions, both in static and dynamic environments. We also present evidence that the indirect genotype/phenotype mapping resulting from genotype editing leads to a better exploration/exploitation compromise of the search process. Therefore, we show that our biologically-inspired model of genotype editing can be used to both facilitate understanding of the evolutionary role of RNA regulation based on genotype editing in biology, and advance the current state of research in Evolutionary Computation.

Keywords:RNA Editing, Genotype Editing, Genetic Algorithms, agent-based modeling, coevolution, indirect genotype/phenotype mapping, dynamic environments, biologicallyinspired computing.

For the full paper please download the pdf version

For more information contact Luis Rocha at Check the Web Design Credits, for due credit.
Last Modified: November 27, 2006